コード例 #1
0
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void start(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
            public override void start(BCF2Encoder encoder, VariantContext vc)
            {
                // TODO
                // TODO this piece of code consumes like 10% of the runtime alone because fo the vc.getGenotypes() iteration
                // TODO
                encodingType = BCF2Type.INT8;
                foreach (Genotype g in vc.Genotypes)
                {
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int[] pls = ige.getValues(g);
                    int[] pls = ige.getValues(g);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type plsType = getFieldEncoder().getType(pls);
                    BCF2Type plsType = FieldEncoder.getType(pls);
                    encodingType = BCF2Utils.maxIntegerType(encodingType, plsType);
                    if (encodingType == BCF2Type.INT32)
                    {
                        break;                         // stop early
                    }
                }

                base.start(encoder, vc);
            }
コード例 #2
0
//JAVA TO C# CONVERTER WARNING: Method 'throws' clauses are not available in .NET:
//ORIGINAL LINE: public void site(final BCF2Encoder encoder, final org.broadinstitute.variant.variantcontext.VariantContext vc) throws java.io.IOException
//JAVA TO C# CONVERTER WARNING: 'final' parameters are not allowed in .NET:
            public override void site(BCF2Encoder encoder, VariantContext vc)
            {
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final Object rawValue = vc.getAttribute(getField(), null);
                object rawValue = vc.getAttribute(Field, null);
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final org.broadinstitute.variant.bcf2.BCF2Type type = getFieldEncoder().getType(rawValue);
                BCF2Type type = FieldEncoder.getType(rawValue);

                if (rawValue == null)
                {
                    // the value is missing, just write in null
                    encoder.encodeType(0, type);
                }
                else
                {
//JAVA TO C# CONVERTER WARNING: The original Java variable was marked 'final':
//ORIGINAL LINE: final int valueCount = getFieldEncoder().numElements(vc, rawValue);
                    int valueCount = FieldEncoder.numElements(vc, rawValue);
                    encoder.encodeType(valueCount, type);
                    FieldEncoder.encodeValue(encoder, rawValue, type, valueCount);
                }
            }